4 files changed, 40 insertions, 255 deletions

diff --git a/math/py-pymc/Makefile b/math/py-pymc/Makefile
index 217e52645bc5..c005b188a158 100644
--- a/math/py-pymc/Makefile
+++ b/math/py-pymc/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	pymc
-PORTVERSION=	2.0
-PORTREVISION=	1
+PORTVERSION=	2.3
 PORTEPOCH=	1
 CATEGORIES=	math python
 MASTER_SITES=	CHEESESHOP
@@ -12,11 +11,37 @@ PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 MAINTAINER=	wenheping@gmail.com
 COMMENT=	Markov Chain Monte Carlo Sampling Toolkit
 
-BUILD_DEPENDS=	${PYNUMPY}
-RUN_DEPENDS:=	${BUILD_DEPENDS}
+LICENSE=	AFL
+LICENSE_NAME=	Academic Free License
+LICENSE_FILE=	${WRKSRC}/LICENSE
+LICENSE_PERMS=	auto-accept dist-mirror dist-sell pkg-mirror pkg-sell
+
+BUILD_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>0:${PORTSDIR}/math/py-matplotlib \
+		${PYTHON_PKGNAMEPREFIX}scipy>0:${PORTSDIR}/science/py-scipy
+LIB_DEPENDS=	liblapack.so:${PORTSDIR}/math/lapack \
+		libblas.so:${PORTSDIR}/math/blas
+RUN_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>0:${PORTSDIR}/math/py-matplotlib \
+		${PYTHON_PKGNAMEPREFIX}scipy>0:${PORTSDIR}/science/py-scipy
+
+OPTIONS_DEFINE=	DOCS
+DOCSDIR=	${PREFIX}/share/doc/py-${PORTNAME}
 
 USE_PYTHON=	yes
 USE_PYDISTUTILS=	yes
+PYDISTUTILS_AUTOPLIST=	yes
+PORTDOCS=	*
+
+post-install:
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/flib.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/cov_funs/distances.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/cov_funs/isotropic_cov_funs.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/incomplete_chol.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/linalg_utils.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/Container_values.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/LazyFunction.so
+	${MKDIR} ${STAGEDIR}${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/docs/*.rst ${STAGEDIR}${DOCSDIR}
 
-NO_STAGE=	yes
 .include <bsd.port.mk>
diff --git a/math/py-pymc/distinfo b/math/py-pymc/distinfo
index b7893c02af9e..a32fba127cac 100644
--- a/math/py-pymc/distinfo
+++ b/math/py-pymc/distinfo
@@ -1,2 +1,2 @@
-SHA256 (pymc-2.0.tar.gz) = 15bbf1e0df9e080d367d639462c4b2b9290826ca069a76ac2bc79d795fe6e653
-SIZE (pymc-2.0.tar.gz) = 1200416
+SHA256 (pymc-2.3.tar.gz) = db029c59d6a04f0c97d88993151c4ee58c76b9ad5c71ead7ee250088ba4cce0d
+SIZE (pymc-2.3.tar.gz) = 13080085
diff --git a/math/py-pymc/pkg-descr b/math/py-pymc/pkg-descr
index 611e0330b425..a817c5a91a2e 100644
--- a/math/py-pymc/pkg-descr
+++ b/math/py-pymc/pkg-descr
@@ -1,11 +1,9 @@
-Bayesian estimation, particularly using Markov chain Monte
-Carlo (MCMC), is an increasingly relevant approach to
-statistical estimation. However, few statistical software
-packages implement MCMC samplers, and they are non-trivial
- to code by hand. pymc is a python package that implements
-the Metropolis-Hastings algorithm as a python class, and is
-extremely flexible and applicable to a large suite of problems.
-pymc includes methods for summarizing output, plotting,
-goodness-of-fit and convergence diagnostics.
+Bayesian estimation, particularly using Markov chain Monte Carlo (MCMC), is an
+increasingly relevant approach to statistical estimation. However, few
+statistical software packages implement MCMC samplers, and they are non-trivial
+to code by hand. pymc is a python package that implements the
+Metropolis-Hastings algorithm as a python class, and is extremely flexible and
+applicable to a large suite of problems.  pymc includes methods for summarizing
+output, plotting, goodness-of-fit and convergence diagnostics.
 
-WWW: https://pypi.python.org/pypi/pymc/
+WWW: http://pypi.python.org/pypi/pymc/
diff --git a/math/py-pymc/pkg-plist b/math/py-pymc/pkg-plist
deleted file mode 100644
index cdb4af11460f..000000000000
--- a/math/py-pymc/pkg-plist
+++ /dev/null
@@ -1,238 +0,0 @@
-%%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.py
-%%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.pyc
-%%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.pyo
-%%PYTHON_SITELIBDIR%%/pymc/Container.py
-%%PYTHON_SITELIBDIR%%/pymc/Container.pyc
-%%PYTHON_SITELIBDIR%%/pymc/Container.pyo
-%%PYTHON_SITELIBDIR%%/pymc/Container_values.so
-%%PYTHON_SITELIBDIR%%/pymc/InstantiationDecorators.py
-%%PYTHON_SITELIBDIR%%/pymc/InstantiationDecorators.pyc
-%%PYTHON_SITELIBDIR%%/pymc/InstantiationDecorators.pyo
-%%PYTHON_SITELIBDIR%%/pymc/LazyFunction.so
-%%PYTHON_SITELIBDIR%%/pymc/MCMC.py
-%%PYTHON_SITELIBDIR%%/pymc/MCMC.pyc
-%%PYTHON_SITELIBDIR%%/pymc/MCMC.pyo
-%%PYTHON_SITELIBDIR%%/pymc/Matplot.py
-%%PYTHON_SITELIBDIR%%/pymc/Matplot.pyc
-%%PYTHON_SITELIBDIR%%/pymc/Matplot.pyo
-%%PYTHON_SITELIBDIR%%/pymc/Model.py
-%%PYTHON_SITELIBDIR%%/pymc/Model.pyc
-%%PYTHON_SITELIBDIR%%/pymc/Model.pyo
-%%PYTHON_SITELIBDIR%%/pymc/Node.py
-%%PYTHON_SITELIBDIR%%/pymc/Node.pyc
-%%PYTHON_SITELIBDIR%%/pymc/Node.pyo
-%%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.py
-%%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.pyc
-%%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.pyo
-%%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.py
-%%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.pyc
-%%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.pyo
-%%PYTHON_SITELIBDIR%%/pymc/ScipyDistributions.py
-%%PYTHON_SITELIBDIR%%/pymc/ScipyDistributions.pyc
-%%PYTHON_SITELIBDIR%%/pymc/ScipyDistributions.pyo
-%%PYTHON_SITELIBDIR%%/pymc/StepMethods.py
-%%PYTHON_SITELIBDIR%%/pymc/StepMethods.pyc
-%%PYTHON_SITELIBDIR%%/pymc/StepMethods.pyo
-%%PYTHON_SITELIBDIR%%/pymc/__init__.py
-%%PYTHON_SITELIBDIR%%/pymc/__init__.pyc
-%%PYTHON_SITELIBDIR%%/pymc/__init__.pyo
-%%PYTHON_SITELIBDIR%%/pymc/database/__init__.py
-%%PYTHON_SITELIBDIR%%/pymc/database/__init__.pyc
-%%PYTHON_SITELIBDIR%%/pymc/database/__init__.pyo
-%%PYTHON_SITELIBDIR%%/pymc/database/base.py
-%%PYTHON_SITELIBDIR%%/pymc/database/base.pyc
-%%PYTHON_SITELIBDIR%%/pymc/database/base.pyo
-%%PYTHON_SITELIBDIR%%/pymc/database/hdf5.py
-%%PYTHON_SITELIBDIR%%/pymc/database/hdf5.pyc
-%%PYTHON_SITELIBDIR%%/pymc/database/hdf5.pyo
-%%PYTHON_SITELIBDIR%%/pymc/database/mysql.py
-%%PYTHON_SITELIBDIR%%/pymc/database/mysql.pyc
-%%PYTHON_SITELIBDIR%%/pymc/database/mysql.pyo
-%%PYTHON_SITELIBDIR%%/pymc/database/no_trace.py
-%%PYTHON_SITELIBDIR%%/pymc/database/no_trace.pyc
-%%PYTHON_SITELIBDIR%%/pymc/database/no_trace.pyo
-%%PYTHON_SITELIBDIR%%/pymc/database/pickle.py
-%%PYTHON_SITELIBDIR%%/pymc/database/pickle.pyc
-%%PYTHON_SITELIBDIR%%/pymc/database/pickle.pyo
-%%PYTHON_SITELIBDIR%%/pymc/database/ram.py
-%%PYTHON_SITELIBDIR%%/pymc/database/ram.pyc
-%%PYTHON_SITELIBDIR%%/pymc/database/ram.pyo
-%%PYTHON_SITELIBDIR%%/pymc/database/sqlite.py
-%%PYTHON_SITELIBDIR%%/pymc/database/sqlite.pyc
-%%PYTHON_SITELIBDIR%%/pymc/database/sqlite.pyo
-%%PYTHON_SITELIBDIR%%/pymc/database/txt.py
-%%PYTHON_SITELIBDIR%%/pymc/database/txt.pyc
-%%PYTHON_SITELIBDIR%%/pymc/database/txt.pyo
-%%PYTHON_SITELIBDIR%%/pymc/decorators.py
-%%PYTHON_SITELIBDIR%%/pymc/decorators.pyc
-%%PYTHON_SITELIBDIR%%/pymc/decorators.pyo
-%%PYTHON_SITELIBDIR%%/pymc/diagnostics.py
-%%PYTHON_SITELIBDIR%%/pymc/diagnostics.pyc
-%%PYTHON_SITELIBDIR%%/pymc/diagnostics.pyo
-%%PYTHON_SITELIBDIR%%/pymc/distributions.py
-%%PYTHON_SITELIBDIR%%/pymc/distributions.pyc
-%%PYTHON_SITELIBDIR%%/pymc/distributions.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/DisasterModel.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/DisasterModel.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/DisasterModel.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/__init__.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/__init__.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/__init__.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/custom_step.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/custom_step.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/custom_step.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_3.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_3.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_3.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/straightlinefit.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/straightlinefit.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/straightlinefit.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.pyo
-%%PYTHON_SITELIBDIR%%/pymc/flib.so
-%%PYTHON_SITELIBDIR%%/pymc/gp/BasisCovariance.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/BasisCovariance.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/BasisCovariance.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/Covariance.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/Covariance.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/Covariance.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/FullRankCovariance.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/FullRankCovariance.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/FullRankCovariance.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/GPutils.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/GPutils.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/GPutils.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/Mean.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/Mean.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/Mean.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/NearlyFullRankCovariance.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/NearlyFullRankCovariance.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/NearlyFullRankCovariance.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/Realization.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/Realization.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/Realization.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/__init__.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/__init__.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/__init__.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/__init__.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/__init__.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/__init__.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/bases.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/bases.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/bases.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/brownian.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/brownian.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/brownian.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/cov_utils.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/cov_utils.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/cov_utils.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/distances.so
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/isotropic_cov_funs.so
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/incomplete_chol.so
-%%PYTHON_SITELIBDIR%%/pymc/gp/linalg_utils.so
-%%PYTHON_SITELIBDIR%%/pymc/graph.py
-%%PYTHON_SITELIBDIR%%/pymc/graph.pyc
-%%PYTHON_SITELIBDIR%%/pymc/graph.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/__init__.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/__init__.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/__init__.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/objectmodel.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/objectmodel.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/objectmodel.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/screen.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/screen.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/screen.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_AM.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_AM.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_AM.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_GP_MCMC.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_GP_MCMC.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_GP_MCMC.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_LazyFunction.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_LazyFunction.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_LazyFunction.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_MCMCSampler.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_MCMCSampler.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_MCMCSampler.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_adaptive.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_adaptive.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_adaptive.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_basiscov.py
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-%%PYTHON_SITELIBDIR%%/pymc/tests/test_binary_step.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_binary_step.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_container.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_container.pyc
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-%%PYTHON_SITELIBDIR%%/pymc/tests/test_convergence.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_convergence.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_convergence.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_cov.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_cov.pyc
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-%%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_instantiation.py
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-%%PYTHON_SITELIBDIR%%/pymc/tests/test_mean.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_mean.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_observation.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_observation.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_observation.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.pyo
-%%PYTHON_SITELIBDIR%%/pymc/utils.py
-%%PYTHON_SITELIBDIR%%/pymc/utils.pyc
-%%PYTHON_SITELIBDIR%%/pymc/utils.pyo
-@dirrm %%PYTHON_SITELIBDIR%%/pymc/tests
-@dirrm %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs
-@dirrm %%PYTHON_SITELIBDIR%%/pymc/gp
-@dirrm %%PYTHON_SITELIBDIR%%/pymc/examples
-@dirrm %%PYTHON_SITELIBDIR%%/pymc/database
-@dirrm %%PYTHON_SITELIBDIR%%/pymc